Cutting out a shape is rendering totally differently to a shape with shape above, even though the paths are identical. Any ideas why this may be happening?
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Sounds to me like your background object(s) are inheriting appearance attributes from the foreground object after you've applied the pathfinder operation.
For example, when you use the 'Intersect' pathfinder operation, the intersecting area is retained - but also inherits the stroke and fill from the foreground item. It looks to me like your 'grain' has inherited a thin stroke from the foreground object - thus making them much thinner and less prominent.
Try selecting your 'grain', and removing any stroke it may have inherited - this may resolve the issue you're experiencing.
If this doesn't work for you, perhaps you could post the file you're working with (with steps to recreate the issue) and I'd be happy to look at it directly.
1. Pre-pathfinder operation (Intersect)
2. After intersection: intersected area inherits stroke and fill of foreground item - NOT background.